[pymvpa] Seg on OSX when using libsvm

[Yaroslav Halchenko]

On Mon, 08 Mar 2010, Fabian Pedregosa wrote:
> test_basic_clf_train_predict
> (mvpa.tests.test_svmkernels.SVMKernelTests) ... Segmentation fault

> Can any mac user reproduce this ?

tried to reproduce on one of the systems we have access to (see details
below, not running Snow Leopard! still known  I believe to have problems with
Python):

But what I know is that our libsvm bindings or libsvm itself does have some
issues which can lead to segfaults (and/or memory leaks) -- I hadn't luck yet
to localize it.  You can valgrind your script (if it is available on your box)
to see if there are related warnings.

P.S. I had to add 'from mvpa.datasets.miscfx import *' to your script
so we get .summmary available for the dataset.

In [1]: run t.py        
Dataset: 2x2 at int32, <sa: targets>
stats: mean=1.5 std=1.11803 var=1.25 min=0 max=3
No per targets/chunks due to KeyError('chunks',)Sequence statistics for 2 entries from set [0, 1]
Counter-balance table for orders up to 2:
Targets/Order O1    |  O2    |
      0:       0 1  |   0 0  |
      1:       0 0  |   0 0  |
Correlations: min=-1 max=-1 mean=-1 sum(abs)=1
[1.0]

In [2]: import mvpa                                                                                                                                 

In [3]: print mvpa.wtf()                                                                                                                            
Current date:   2010-03-08 13:37
PyMVPA:
 Version:       0.5.0.dev
 Path:          /Users/yoh/proj/pymvpa/mvpa/__init__.pyc
 Version control (GIT):
  Status:
   # On branch master
   nothing to commit (working directory clean)
  Reference:
   d32bba93da5f02d0ef986e4cb40c4cdbed723455 HEAD
   d32bba93da5f02d0ef986e4cb40c4cdbed723455 refs/remotes/origin/HEAD
  Difference from last release 0.5.0.dev:
    332 files changed, 46592 insertions(+), 10344 deletions(-)
SYSTEM:
 OS:            posix Darwin 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386
 Distribution:   10.5.8/i386
EXTERNALS:
 Present:       cPickle, ctypes, good scipy.stats.rv_discrete.ppf, griddata, gzip, hcluster, libsvm, libsvm verbosity control, nose, numpy, reportlab, rpy2, running ipython env, scipy, weave
 Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, good scipy.stats.rdist, h5py, lars, lxml, matplotlib, mdp, mdp ge 2.4, nibabel, nifti, nifti ge 0.20090205.1, nipy, openopt, pprocess, pylab, pylab plottable, pywt, pywt wp reconstruct, pywt wp reconstruct fixed, rpy, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun, shogun.krr, shogun.lightsvm, shogun.mpd, shogun.svrlight
 Versions of critical externals:
  ipython     : 0.8.1
  reportlab   : 2.1
  scipy       : 0.7.0
  numpy       : 1.3.0
  rpy2        : 2.0.3
  ctypes      : 1.0.3
  numpy       : 1.3.0
RUNTIME:
 PyMVPA Environment Variables:
  PYTHONPATH          : "/Users/yoh/proj/pymvpa"
....



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Yaroslav Halchenko              /(   )\               ICQ#: 60653192
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